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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ), 'gf_id' => 'HOM05D001182', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001182' ), 'data_identifier' => 'HOM05D001182', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001182', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '527', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35990' => 'bna', 'A04p16350' => 'bna', 'A05p20870' => 'bna', 'A06p34360' => 'bna', 'A07p37600' => 'bna', 'A09p57980' => 'bna', 'Aa31LG10G4820' => 'aar', 'Aa31LG11G2820' => 'aar', 'Aa31LG3G18180' => 'aar', 'Aa31LG3G4170' => 'aar', 'Aa31LG4G9270' => 'aar', 'Aa31LG8G5180' => 'aar', 'Aa31LG9G18050' => 'aar', 'Aa31sc286G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.531' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2081' => 'aag', 'Actinidia00212' => 'ach', 'Actinidia06836' => 'ach', 'Actinidia19839' => 'ach', 'Actinidia19840' => 'ach', 'Actinidia19841' => 'ach', 'Actinidia23693' => 'ach', 'Actinidia37804' => 'ach', 'Actinidia37805' => 'ach', 'Actinidia39048' => 'ach', 'Ah.01g002710' => 'amhyb', 'Ah.02g115030' => 'amhyb', 'Ah.02g115040' => 'amhyb', 'Ah.12g059800' => 'amhyb', 'AL1G55570' => 'aly', 'AL2G30850' => 'aly', 'AL3G31630' => 'aly', 'AL4G10960' => 'aly', 'AL6G34650' => 'aly', 'Aqoxy1G00538' => 'aox', 'Aqoxy3G00002' => 'aox', 'Aqoxy3G00273' => 'aox', 'Aqoxy5G02433' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7S5TTX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AY1CAG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C8HI84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JMCM5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MSII7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PP7MBT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SMR6SK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6BJG4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UK23IF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YMP0XI' => 'arhy', 'AT1G48840' => 'ath', 'AT1G71240' => 'ath', 'AT2G21720' => 'ath', 'AT3G18350' => 'ath', 'AT5G23390' => 'ath', 'ATR0124G039' => 'atr', 'ATR0584G139' => 'atr', 'ATR0693G029' => 'atr', 'ATR0697G161' => 'atr', 'ATR1125G069' => 'atr', 'Atru.chr11.41' => 'acertr', 'Atru.chr2.1478_Atru.chr2.1479' => 'acertr', 'Atru.chr6.839_Atru.chr6.840' => 'acertr', 'Atru.chr9.846' => 'acertr', 'AUR62015048' => 'cqu', 'AUR62017507' => 'cqu', 'AUR62017755' => 'cqu', 'AUR62018247' => 'cqu', 'AUR62025840' => 'cqu', 'AUR62029873' => 'cqu', 'AUR62030684' => 'cqu', 'AUR62032896' => 'cqu', 'AUR62041190' => 'cqu', 'AUR62044161' => 'cqu', 'BcaB02g11305' => 'bca', 'BcaB03g14882' => 'bca', 'BcaB06g27783' => 'bca', 'BcaB08g35004' => 'bca', 'BcaC02g08771' => 'bca', 'BcaC05g27550' => 'bca', 'BcaC07g41118' => 'bca', 'BcaC08g46560' => 'bca', 'BcaC09g48793' => 'bca', 'BcaNung03726' => 'bca', 'BolC1t04548H' => 'bol', 'BolC4t26678H' => 'bol', 'BolC5t32249H' => 'bol', 'BolC6t39592H' => 'bol', 'BolC7t44941H' => 'bol', 'BolC8t51686H' => 'bol', 'BraA01t03680Z' => 'bra', 'BraA04t17273Z' => 'bra', 'BraA05t20992Z' => 'bra', 'BraA06t26366Z' => 'bra', 'BraA07t31321Z' => 'bra', 'BraA09t41188Z' => 'bra', 'C01p45860' => 'bna', 'C04p50840' => 'bna', 'C05p35360' => 'bna', 'C06p45360' => 'bna', 'C07p44170' => 'bna', 'C08p41190' => 'bna', 'CAN.G1425.7' => 'can', 'CAN.G1577.8' => 'can', 'CAN.G187.8' => 'can', 'CAN.G610.67' => 'can', 'CANSAT54G1880' => 'cansat', 'CANSAT78G0095' => 'cansat', 'CANSAT78G1258' => 'cansat', 'CANSAT80G0953' => 'cansat', 'CARHR038840' => 'chi', 'CARHR064540' => 'chi', 'CARHR093700' => 'chi', 'CARHR112770' => 'chi', 'CARHR119410' => 'chi', 'CARHR190120' => 'chi', 'Carub.0001s3798' => 'cru', 'Carub.0002s1812' => 'cru', 'Carub.0003s1812' => 'cru', 'Carub.0004s0077' => 'cru', 'Carub.0006s2117' => 'cru', 'Ca_00081_v3' => 'car', 'Ca_08297_v3' => 'car', 'Ca_11279_v3' => 'car', 'Ca_25484_v3' => 'car', 'Cc00_g34250' => 'ccan', 'Cc02_g22390' => 'ccan', 'Cc04_g07050' => 'ccan', 'Cc05_g02290' => 'ccan', 'Cc05_g02300' => 'ccan', 'Cc11_g01190' => 'ccan', 'CDE02G2350' => 'cde', 'CDE04G0007' => 'cde', 'CDE04G0254' => 'cde', 'CDE04G1226' => 'cde', 'CDE06G1628' => 'cde', 'CDE07G1055' => 'cde', 'CDE12G0522' => 'cde', 'Cfa005531' => 'cfa', 'Cfa017694' => 'cfa', 'Ciclev10000484m.g' => 'ccl', 'Ciclev10014467m.g' => 'ccl', 'Ciclev10019113m.g' => 'ccl', 'Ciclev10019164m.g' => 'ccl', 'CiPaw.06G148200' => 'cil', 'CiPaw.09G168900' => 'cil', 'CiPaw.15G131500' => 'cil', 'CiPaw.16G000800' => 'cil', 'CiPaw.16G087100' => 'cil', 'ClCG01G007950' => 'cla', 'ClCG04G005450' => 'cla', 'ClCG06G014750' => 'cla', 'ClCG09G013930' => 'cla', 'COL.COLO4_17879' => 'col', 'COL.COLO4_28615' => 'col', 'COL.COLO4_32829' => 'col', 'COL.COLO4_32830' => 'col', 'COL.COLO4_33140' => 'col', 'COL.COLO4_34317' => 'col', 'Cpa.g.c31165' => 'cpa', 'Cpa.g.c32648' => 'cpa', 'Cpa.g.c34438' => 'cpa', 'Cpa.g.sc113.70' => 'cpa', 'Cpa.g.sc161.17' => 'cpa', 'Cpa.g.sc2.1' => 'cpa', 'Cpa.g.sc2.2' => 'cpa', 'Cpa.g.sc3.504' => 'cpa', 'CsaV3_1G003890' => 'csa', 'CsaV3_1G044980' => 'csa', 'CsaV3_1G044990' => 'csa', 'CsaV3_4G012130' => 'csa', 'CsaV3_5G021920' => 'csa', 'CSS0001986' => 'camsi', 'CSS0002600' => 'camsi', 'CSS0008710' => 'camsi', 'CSS0017219' => 'camsi', 'CSS0046127' => 'camsi', 'CSS0048604' => 'camsi', 'DCAR_002616' => 'dca', 'DCAR_013991' => 'dca', 'DCAR_020656' => 'dca', 'DCAR_023209' => 'dca', 'DCAR_030347' => 'dca', 'DCAR_030349' => 'dca', 'Dinv12814' => 'din', 'Dinv19358' => 'din', 'Dinv24265' => 'din', 'Dinv25062' => 'din', 'Dinv28112' => 'din', 'Duzib068G1307' => 'dzi', 'Duzib132G0224' => 'dzi', 'Duzib132G0513' => 'dzi', 'Duzib177G0751' => 'dzi', 'Duzib205G0785' => 'dzi', 'ECA233G2483' => 'eca', 'ECA233G4533' => 'eca', 'ECA234G2900' => 'eca', 'ECA236G1096' => 'eca', 'ECA240G2723' => 'eca', 'ECA248G3079' => 'eca', 'EL10Ac5g11456' => 'bvu', 'EL10Ac5g11742' => 'bvu', 'EL10Ac9g22713' => 'bvu', 'EL10Ac9g23019' => 'bvu', 'Eucgr.A02130' => 'egr', 'Eucgr.B00730' => 'egr', 'Eucgr.G00608' => 'egr', 'Eucgr.G02612' => 'egr', 'Eucgr.K02228' => 'egr', 'FAN04G1120' => 'fan', 'FAN04G2731' => 'fan', 'FAN07G1452' => 'fan', 'FAN08G1003' => 'fan', 'FAN08G2833' => 'fan', 'FAN13G0534' => 'fan', 'FAN13G3273' => 'fan', 'FAN17G0684' => 'fan', 'FAN18G0972' => 'fan', 'FAN18G2314' => 'fan', 'FAN19G0060' => 'fan', 'FAN23G1747' => 'fan', 'FAN26G0742' => 'fan', 'FAN28G1784' => 'fan', 'FvH4_1g28470' => 'fve', 'FvH4_4g37320' => 'fve', 'FvH4_5g11960' => 'fve', 'FvH4_5g29650' => 'fve', 'Glyma.01G121100' => 'gma', 'Glyma.01G123700' => 'gma', 'Glyma.06G038100' => 'gma', 'Glyma.07G092600' => 'gma', 'Glyma.08G185700' => 'gma', 'Glyma.09G183600' => 'gma', 'Glyma.10G289000' => 'gma', 'Glyma.12G026200' => 'gma', 'Glyma.15G047100' => 'gma', 'Glyma.15G225600' => 'gma', 'Glyma.16G037800' => 'gma', 'Glyma.19G114800' => 'gma', 'Glyma.20G099900' => 'gma', 'Gohir.A01G177900' => 'ghi', 'Gohir.A03G211100' => 'ghi', 'Gohir.A04G109700' => 'ghi', 'Gohir.A08G093900' => 'ghi', 'Gohir.A08G094000' => 'ghi', 'Gohir.A08G219700' => 'ghi', 'Gohir.A09G048200' => 'ghi', 'Gohir.A11G231500' => 'ghi', 'Gohir.D01G168700' => 'ghi', 'Gohir.D02G232700' => 'ghi', 'Gohir.D04G149900' => 'ghi', 'Gohir.D08G105200' => 'ghi', 'Gohir.D08G236600' => 'ghi', 'Gohir.D09G049300' => 'ghi', 'Gohir.D11G242800' => 'ghi', 'Gorai.002G209500' => 'gra', 'Gorai.004G112100' => 'gra', 'Gorai.004G251800' => 'gra', 'Gorai.005G260500' => 'gra', 'Gorai.006G060500' => 'gra', 'Gorai.007G257000' => 'gra', 'Gorai.012G136500' => 'gra', 'GSVIVG01008298001' => 'vvi', 'GSVIVG01022994001' => 'vvi', 'GSVIVG01029954001' => 'vvi', 'GSVIVG01034353001' => 'vvi', 'HanXRQChr03g0066821' => 'han', 'HanXRQChr08g0227461' => 'han', 'HanXRQChr11g0337521' => 'han', 'HanXRQChr11g0348171' => 'han', 'HanXRQChr13g0398981' => 'han', 'HanXRQChr16g0513941' => 'han', 'Haze_01650' => 'cav', 'Haze_01651' => 'cav', 'Haze_17402' => 'cav', 'Haze_18690' => 'cav', 'Haze_20445' => 'cav', 'Hma1.2p1_0513F.1_g169620' => 'hma', 'Hma1.2p1_0557F.1_g178390' => 'hma', 'Hma1.2p1_0653F.1_g196230' => 'hma', 'HPP92_001083' => 'vpl', 'HPP92_014420' => 'vpl', 'HPP92_014425' => 'vpl', 'HPP92_014543' => 'vpl', 'HPP92_023446' => 'vpl', 'HPP92_023447' => 'vpl', 'HPP92_023448' => 'vpl', 'HPP92_023449' => 'vpl', 'HPP92_023464' => 'vpl', 'HPP92_027473' => 'vpl', 'Hund01588' => 'sun', 'Hund10255' => 'sun', 'Lalb_Chr14g0364681' => 'lal', 'Lalb_Chr14g0371111' => 'lal', 'Lalb_Chr15g0090641' => 'lal', 'Lalb_Chr21g0307421' => 'lal', 'Lalb_Chr24g0397851' => 'lal', 'Lj1A1063G39' => 'lonja', 'Lj1g0018369' => 'lja', 'Lj2g0006478' => 'lja', 'Lj3A844T50' => 'lonja', 'Lj5A149T47' => 'lonja', 'Lj5g0022468' => 'lja', 'Lj6g0002068' => 'lja', 'Lj9A307T42' => 'lonja', 'Lsat_1_v5_gn_1_56040' => 'lsa', 'Lsat_1_v5_gn_5_109401' => 'lsa', 'Lsat_1_v5_gn_6_31760' => 'lsa', 'Lsat_1_v5_gn_7_78320' => 'lsa', 'Lsat_1_v5_gn_8_146681' => 'lsa', 'Lsat_1_v5_gn_9_118280' => 'lsa', 'Manes.04G161000' => 'mes', 'Manes.05G113577' => 'mes', 'Manes.07G014700' => 'mes', 'Manes.09G137900' => 'mes', 'Mapoly0004s0069' => 'mpo', 'Mapoly0058s0023' => 'mpo', 'MBI06_g22567_MAGBIO' => 'mbi', 'MBI06_g40826_MAGBIO' => 'mbi', 'MBI09_g06383_MAGBIO' => 'mbi', 'MBI15_g00960_MAGBIO' => 'mbi', 'MBI16_g32667_MAGBIO' => 'mbi', 'MD06G1216900' => 'mdo', 'MD08G1227800' => 'mdo', 'MD12G1008600' => 'mdo', 'MD13G1001200' => 'mdo', 'MD14G1006000' => 'mdo', 'MD14G1227300' => 'mdo', 'MD15G1421600' => 'mdo', 'Medtr1g115260' => 'mtr', 'Medtr2g007330' => 'mtr', 'Medtr6g084190' => 'mtr', 'Medtr7g006750' => 'mtr', 'Medtr7g086350' => 'mtr', 'MELO3C005083.2' => 'cme', 'MELO3C008818.2' => 'cme', 'MELO3C010089.2' => 'cme', 'MELO3C017313.2' => 'cme', 'Migut.J00771' => 'egut', 'Migut.L00591' => 'egut', 'Migut.L00606' => 'egut', 'Migut.N01040' => 'egut', 'MSTRG.4520' => 'ama', 'MSTRG.5232' => 'ama', 'MSTRG.8099' => 'ama', 'Nitab4.5_0000057g0180' => 'nta', 'Nitab4.5_0000112g0010' => 'nta', 'Nitab4.5_0000112g0020' => 'nta', 'Nitab4.5_0000112g0030' => 'nta', 'Nitab4.5_0002245g0160' => 'nta', 'Nitab4.5_0002906g0040' => 'nta', 'Nitab4.5_0003034g0030' => 'nta', 'Nitab4.5_0003034g0050' => 'nta', 'Nitab4.5_0003034g0060' => 'nta', 'Nitab4.5_0003715g0070' => 'nta', 'Nitab4.5_0003867g0040' => 'nta', 'Nitab4.5_0005224g0020' => 'nta', 'Nitab4.5_0007398g0010' => 'nta', 'Nitab4.5_0011195g0030' => 'nta', 'Nn1g08676' => 'nnu', 'Nn3g17867' => 'nnu', 'Nn4g23870' => 'nnu', 'Nn4g25065' => 'nnu', 'Nn5g28124' => 'nnu', 'Nn6g32390' => 'nnu', 'Oeu001002.1' => 'oeu', 'Oeu001003.1' => 'oeu', 'Oeu008242.1' => 'oeu', 'Oeu008885.2' => 'oeu', 'Oeu035460.2' => 'oeu', 'Oeu036769.1' => 'oeu', 'Oeu044651.1' => 'oeu', 'Os01g0869000' => 'osa', 'Os02g0637800' => 'osa', 'Os03g0157700' => 'osa', 'Os04g0677400' => 'osa', 'Os05g0264200' => 'osa', 'Os10g0127700' => 'osa', 'Peaxi162Scf00011g00357' => 'pax', 'Peaxi162Scf00011g00358' => 'pax', 'Peaxi162Scf00015g01041' => 'pax', 'Peaxi162Scf00564g00214' => 'pax', 'Peaxi162Scf00655g00329' => 'pax', 'Peaxi162Scf00753g00430' => 'pax', 'PGR042G0576' => 'pgr', 'PGR042G2001' => 'pgr', 'PGR042G2672' => 'pgr', 'PGR044G1649' => 'pgr', 'PGR142G3788' => 'pgr', 'PGSC0003DMG400014571' => 'stu', 'PGSC0003DMG402005724' => 'stu', 'Phvul.001G114200' => 'pvu', 'Phvul.004G156200' => 'pvu', 'Phvul.006G214050' => 'pvu', 'Phvul.007G012100' => 'pvu', 'Potri.001G210200' => 'ptr', 'Potri.008G003000' => 'ptr', 'Potri.012G055800' => 'ptr', 'Potri.013G062700' => 'ptr', 'Potri.015G046500' => 'ptr', 'Pp3c11_5990' => 'ppa', 'Pp3c14_16340' => 'ppa', 'Pp3c17_20110' => 'ppa', 'Pp3c1_33350' => 'ppa', 'Pp3c2_26720' => 'ppa', 'Pp3c7_25470' => 'ppa', 'Prupe.1G351500' => 'ppe', 'Prupe.1G566800' => 'ppe', 'Prupe.5G222100' => 'ppe', 'Prupe.7G010400' => 'ppe', 'Psat0s4033g0120' => 'psa', 'Psat1g034680' => 'psa', 'Psat1g224520' => 'psa', 'Psat6g234520' => 'psa', 'PSO017G4243' => 'pso', 'PSO017G4704' => 'pso', 'PSO063G4221' => 'pso', 'PSO170G3364' => 'pso', 'PSO384G1027' => 'pso', 'PSO478G5086' => 'pso', 'PSO782G0687' => 'pso', 'QL03p073653' => 'qlo', 'QL07p017742' => 'qlo', 'QL10p025522' => 'qlo', 'QL11p000326' => 'qlo', 'RcHm_v2.0_Chr3g0496361' => 'rch', 'RcHm_v2.0_Chr3g0496371' => 'rch', 'RcHm_v2.0_Chr4g0447161' => 'rch', 'RcHm_v2.0_Chr4g0447171' => 'rch', 'RcHm_v2.0_Chr7g0185541' => 'rch', 'RcHm_v2.0_Chr7g0222711' => 'rch', 'Rhsim03G0052300' => 'rsi', 'Rhsim08G0132600' => 'rsi', 'Rhsim11G0130000' => 'rsi', 'Rhsim12G0090100' => 'rsi', 'Sabra01G0162400' => 'sbr', 'Sabra12G0039600' => 'sbr', 'Sabra13G0055900' => 'sbr', 'Sabra15G0039200' => 'sbr', 'SalBow1G5299' => 'sbo', 'SalBow2G3290' => 'sbo', 'SalBow3G4185' => 'sbo', 'SalBow6G4578' => 'sbo', 'SalBow6G5030' => 'sbo', 'Sc03g0006140' => 'sci', 'Sc12g0007640' => 'sci', 'Sc21g0000760' => 'sci', 'Sc25g0001500' => 'sci', 'Sed0000377' => 'sed', 'Sed0007065' => 'sed', 'Sed0008850' => 'sed', 'Sed0011486' => 'sed', 'Sed0012377' => 'sed', 'Sed0022471' => 'sed', 'SEGI_01751' => 'sgi', 'SEGI_18873' => 'sgi', 'SEGI_30096' => 'sgi', 'SGA_v2.0_scaffold145G36071' => 'sas', 'SGA_v2.0_scaffold31G12790' => 'sas', 'SGA_v2.0_scaffold3G01734' => 'sas', 'SGA_v2.0_scaffold407G51065' => 'sas', 'SHI14923' => 'shi', 'SMO117G0194' => 'smo', 'SMO347G0651' => 'smo', 'Solyc01g104300.3' => 'sly', 'Solyc02g049108.1' => 'sly', 'Solyc02g050180.4' => 'sly', 'Solyc03g119400.3' => 'sly', 'Solyc04g007290.4' => 'sly', 'Solyc05g009240.3' => 'sly', 'Sopen01g046740' => 'spe', 'Sopen02g008400' => 'spe', 'Sopen03g038260' => 'spe', 'Sopen04g002350' => 'spe', 'Sopen05g004970' => 'spe', 'Sp1g35730' => 'spa', 'Sp2g23780' => 'spa', 'Sp3g16460' => 'spa', 'Sp4g00880' => 'spa', 'Sp5g26440' => 'spa', 'TAR371G0086' => 'tar', 'TAR371G0313' => 'tar', 'TAR371G0900' => 'tar', 'TAR622G0520' => 'tar', 'TAR622G0796' => 'tar', 'TAR628G0505' => 'tar', 'TAR633G1962' => 'tar', 'TAR665G0001' => 'tar', 'THA.LOC104800080' => 'tha', 'THA.LOC104800240' => 'tha', 'THA.LOC104800626' => 'tha', 'THA.LOC104804881' => 'tha', 'THA.LOC104805994' => 'tha', 'THA.LOC104809831' => 'tha', 'THA.LOC104817120' => 'tha', 'Thecc.02G039700' => 'tca', 'Thecc.02G152300' => 'tca', 'Thecc.03G036600' => 'tca', 'Thecc.05G244300' => 'tca', 'Thhalv10000626m.g' => 'esa', 'Thhalv10003718m.g' => 'esa', 'Thhalv10011279m.g' => 'esa', 'Thhalv10018126m.g' => 'esa', 'Thhalv10020186m.g' => 'esa', 'TPR.G15168' => 'tpr', 'TPR.G17862' => 'tpr', 'TPR.G2100' => 'tpr', 'TPR.G4064' => 'tpr', 'TWI14G1019' => 'twi', 'TWI60G1338' => 'twi', 'TWI77G0690' => 'twi', 'TWI81G0083' => 'twi', 'unitig_37.g12826' => 'ugi', 'unitig_52.g17435' => 'ugi', 'unitig_52.g17436' => 'ugi', 'unitig_699.g19413' => 'ugi', 'vmacro01766' => 'vma', 'vmacro07559' => 'vma', 'vmacro16165' => 'vma', 'vmacro17711' => 'vma', 'VMungo0464G1733' => 'vmu', 'VMungo0540G0659' => 'vmu', 'VMungo0720G1639' => 'vmu', 'VMungo1383G2305' => 'vmu', 'Zm00001eb062010' => 'zma', 'Zm00001eb146600' => 'zma', 'Zm00001eb185620' => 'zma', 'Zm00001eb403230' => 'zma', 'Zm00001eb433740' => 'zma' ) $gf_id = 'HOM05D001182' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001182' ) $data_identifier = 'HOM05D001182' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 8, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 10, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 6, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 8, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 13, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 3, 'vpl' => (int) 10, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 14, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 5, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb433740' $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